Robert Farley has a run-down of how unlikely ( but not impossible) a scenario this would have been. Note though that the attack was carried out with the assistance of several Pakistani Navy officers, so if they had, in fact gotten control of the vessel, the corsairs could, have conceivably done some mischief in the very, very brief window before the ship would have been sunk. "Mischief" might not even involve leaving harbor (or even the pier) if the general vicinity of a target was already known. The C-102 missiles the ship is armed with have a range of up to 500 kilometers depending on version. The Long War Journal has an account of the incident including info from a press release by AQIS and it is claimed that the operation was much more elaborate and involved a large number of Jihadis in uniform. One aspect of the attack was to have crewmen loyal to Al Qaeda take over the ship's main gun and fire rounds at USNS Supply which was scheduled to be doing refueling drills with Zulfiquar.

While the 3 inch gun would be unlikely to sink the big ship, fires and explosions on a combination Tanker/ Ammunition ship have great potential to get out of hand. The fact that USNS Supply is one of only 4 of the big AOEs left would have made any damage to the ship a severe blow to the Navy's ability to supply ships on far flung stations.

This is quite disturbing of course, but the large number of double agents involved is even more troubling.

Tactical weapons are, by necessity, deployed with the military forces, so the chances of them falling into jihadist hands is much greater. To get some idea of what these can do we'll look again to the well photographed shot of 'Atomic Annie' popping off a 15 kiloton W-9 shell.

Note the size of the weapon, 55 inches long 11 inches wide and 850 pounds. The later W-19 round for the same gun was only 600 pounds and had a slightly higher yield. This is not a particularly powerful nuke, but I'm being conservative in estimating what the Pakistani's are capable of. More disturbing; the size of the weapon is such that it could easily be smuggled into a city, and while the blast damage of such a weapon would be limited compared to a strategic nuke detonated at altitude, the fallout from a ground burst would be horrific.

The prospect of a terrorist nuclear attack, is as great as ever, so it's probably a good idea to look into how to prepare for modest sized ground bursts. RAND has a paper on that, available in PDF format here.